RoseTTAFold All Atom | Folding proteins with DNA using RoseTTAFold | Full Tutorial

In this video we demonstrate how to fold two proteins in complex with DNA using the RoseTTAFold All-Atom on the Neurosnap platform. The Neurosnap platform is designed to make bioinformatics easy for wet lab and non technical biologists.
#biology #biochemistry #proteinstructure #molecularbiology #deeplearning
Check out Neurosnap: neurosnap.ai/

[@xmao403]

The analysis of DNA and protein interaction is important.

[@sreeram6416]

sir is there any tool that can tell us the predicted rna sequence aptamers that can bind to our defined motifs or sequences

[@NeurosnapInc]

RFdiffusion All-Atom should in theory be able to do this but is currently not usable due to various bugs with the code base. Alternatively, RFdiffusion-v2 on Neurosnap can generate peptide binders against a given target but does not support nucleotides.

[@sreeram6416]

sir can we do docking of rna and protein also

[@NeurosnapInc]

Great question, currently the Uracil nucleotide is not supported by RF-AA but on the Neurosnap platform we have a current workaround where we convert the RNA into its equivalent ssDNA. While sub-optimal,, this is a fairly useful method that can be used to approximate what the protein-RNA interaction would look like. We are currently working on a solution to make it fully compatible with various types of RNA.